Ali Harbi Ali, 25, from London, has been charged with murder and preparing acts of terrorism, the Crown Prosecution Service (CPS) said. Sir David, who represented Southend West in Essex, was stabbed to death last Friday as he was meeting his constituents at Belfairs Methodist Church in Leigh-on-Sea.
Ali Harbi Ali remains in custody and is due to appear at Westminster Magistrates' Court on Thursday afternoon.
In a statement, Nick Price, of the CPS, said: "The CPS has authorised charges against Ali Harbi Ali for the murder of MP Sir David Amess on Friday 15 October 2021.
“We will submit to the court that this murder has a terrorist connection, namely that it had both religious and ideological motivations.
"He has also been charged with the preparation of terrorist acts.
“This follows a review of the evidence gathered by the Metropolitan Police in its investigation.
"The Crown Prosecution Service reminds all concerned that criminal proceedings against Mr Ali are active and that he has a right to a fair trial."
Metropolitan Police Assistant Commissioner Matt Jukes said the force’s Counter Terrorism Command had been "working around the clock”.
He added a number of London addresses have been searched and detectives have analysed digital devices and CCTV footage.
The Met chief said there have been no other arrests and police are not seeking anyone else.
Mr Jukes said: "Today's charge is a significant milestone in the case, but the work from my colleagues in the Met's Counter Terrorism Command will continue apace."
He added: “It remains the case that no other arrest has been made and at this time we are not seeking anybody else in relation to this incident.”
Speaking outside New Scotland Yard, Mr Jukes added: "A large team of detectives have been working around the clock to find out as much as we can about what happened and why.
"That work has included searches at a number of London addresses.
"Our advanced forensics team analysed digital devices and carried out a painstaking review of CCTV footage.
"If there are members of the public who have further information that might help the investigation, I would urge them to come forward.
"Every piece of information in investigations like these is important and you will not be wasting our time."
Sir David became the Tory MP for Basildon in 1983 and served in the constituency for 14 years.
At the 1997 general election, he stood in the Southend West seat and remained there as an MP until his death.
On Monday, MPs returned to parliament and paid tributes to Sir David in the House of Commons.
Prime Minister Boris Johnson confirmed Southend would be granted city status, in recognition of his decades-long campaign for the seaside town to be given the honour.